To open protocols as a printer-friendly format, go to http://lowepowerlab.ucdavis.edu/protocols/

Protocols

Lab protocols for the Lowe-Power lab

Lab Management & Maintenence

Important information for all full-timers!

• Chemical Management
• Purchasing
• What to do if the building loses electricity

Undergrad Relevant Information

• Preparing sterile supplies
• Shelf stocking
• Autoclave

Familiarize Yourself with Common Lab Terms

Lowe-Power Lab Glossary

This link gives access for viewing and leaving comments if you have questions or want to suggest changes.

Molecular Biology

• DNA Electrophoresis
• Plasmid and DNA sequence management in the lab Benchling folder
• PCRs to detect & classify Ralstonia
• Primer Design with PrimerBlast
• Overview of cloning tools for Ralstonia
• Gene deletion in *Ralstonia *
• Gibson assembly
• Colony PCR
• Sanger Sequencing

• Step-by-step guide to gene deletion (protocols.io by Noah Guillome)

  https://www.protocols.io/view/unmarked-gene-deletion-ralstonia-primer-design-ewov1mrp2vr2/v1
  https://www.protocols.io/view/unmarked-gene-deletion-ralstonia-upstream-amp-down-261ge8q6yg47/v1
  https://www.protocols.io/view/unmarked-gene-deletion-ralstonia-gibson-assembly-a-8epv5owx6g1b/v1
  https://www.protocols.io/view/unmarked-gene-deletion-ralstonia-colony-pcr-n92ldnojnv5b/v1
  https://www.protocols.io/view/unmarked-gene-deletion-ralstonia-electroporation-t-5jyl8q3z6l2w/v1
  https://www.protocols.io/view/unmarked-gene-deletion-ralstonia-external-ralstoni-8epv5k73jv1b/v1
  

In addition to our lab protocols, here are resources that are very useful:

• A Primer on Cloning in E. coli by Michael Nonet at Wash U

Microbiology

• General growth of Ralstonia
• Glycerol stocks (-70C)
• Media recipes
  • [] Add table of contents
• [draft] Buffers and Reagents
• Antibiotics
• Chemically competent E. coli - Mix&Go
• Electrocompetent Ralstonia cells
• Natural transformation of Ralstonia
• Conjugation with E. coli WM3064
• [] Growth curve: test tube
• Growth curve: 96 well microplate
• Dilution plating & colony forming units
• Competition Assay This is written for an in planta assay, but could be adapted to in vitro experiments.

Plants

• Tomato: sowing, growing, & transplanting
• Tomato: petiole inoculation
• Tomato: soil soak inoculation
• Tomato: xylem sap harvesting by root pressure
• [] Melon: inoculations
• Measuring wilt symptoms for a disease progress assay
• Colonization: tomato stem
• Competition Assay This is written for cut-petiole competitions, but it can be adapted to soil soak.
• [] Colonization: tomato roots
• [w.i.p.] Growing Tomato for seed
• [] Tobacco Mosaic Virus & other things to worry about

Workbooks and Excel templates

• (Gibson) assembly
• bacterial density
• chemistry calculations
• PCR
• 96- and 24-well microplate templates

KBase and Bioinformatics

• Useful KBase narratives

GitHub

• Best Practices for Markdown / editing protocols
• [draft] Git and Github e.g. How to Update lab protocols with forking, committing, and pushing

References & Acknowledgement (and great resources)

This repo is inspired by Mark Mandel’s lab protocol repo. What a gem. Additional labs with great protocol repositories are Barrick lab, ..

I also highly recommend using the AddGene website as a resource on molecular biology. http://www.addgene.org/mol-bio-reference/

This work is licensed under a Creative Commons Attribution 4.0 International License.